Free Energy Analysis of Peptide-Induced Pore Formation in Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations

Antimicrobial peptides (AMPs) are attractive materials
for combating
the antimicrobial resistance crisis because they can kill target microbes
by directly disrupting cell membranes. Although thousands of AMPs
have been discovered, their molecular mechanisms of action are still
poorly understood. One broad mechanism for membrane disruption is
the formation of membrane-spanning hydrophilic pores which can be
stabilized by AMPs. In this study, we use molecular dynamics simulations
to investigate the thermodynamics of pore formation in model single-component
lipid membranes in the presence of one of three AMPs: aurein 1.2,
melittin and magainin 2. To overcome the general challenge of modeling
long time scale membrane-related behaviors, including AMP binding,
clustering, and pore formation, we develop a generalizable methodology
for sampling AMP-induced pore formation. This approach involves the
long equilibration of peptides around a pore created with a nucleation
collective variable by performing coarse-grained simulations, then
backmapping equilibrated AMP-membrane configurations to all-atom resolution.
We then perform all-atom simulations to resolve free energy profiles
for pore formation while accurately modeling the interplay of lipid–peptide–solvent
interactions that dictate pore formation free energies. Using this
approach, we quantify free energy barriers for pore formation without
direct biases on peptides or whole lipids, allowing us to investigate
mechanisms of pore formation for these 3 AMPs that are a consequence
of unbiased peptide diffusion and clustering. Further analysis of
simulation trajectories then relates variations in pore lining by
AMPs, AMP-induced lipid disruptions, and salt bridges between AMPs
to the observed pore formation free energies and corresponding mechanisms.
This methodology and mechanistic analysis have the potential to generalize
beyond the AMPs in this study to improve our understanding of pore
formation by AMPs and related antimicrobial materials.